Hi Hunter,
You should look into parmed and cpptraj for this. Fixatomorder, or define
solvent or set molecules were some of the options that have helped me in
the past for this (although it's been a while, so please check the names
above, particular i don't remember the exact command to define the solvent
or the molecules, but definitely the functionality exists). You can
construct a new prmtop to use for your analysis and that should fix your
issues in my experience
All the best,
Clorice
On Tue, Nov 8, 2022 at 1:40 PM Hunter Wilson via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I was running a trajectory of a protein with parameters that I made with
> the MCPB.py tool and was running analysis with cpptraj. Whenever I try and
> 'autoimage' water molecules back into the center of the box, I get the
> following message:
>
> ACTION SETUP FOR PARM 'hydrox_wt_solv.prmtop' (1 actions):
> 0: [autoimage anchor :1-263]
> Warning: Topology hydrox_wt_solv.prmtop does not contain molecule
> information
> Warning: Setup incomplete for [autoimage]: Skipping
>
> I've used MCPB.py and never run into this problem before. When I look at my
> trajectories, there aren't any weird bonds and the protein isn't blowing up
> or performing any unphysical actions. Any help with the issue would be
> greatly appreciated. I've attached my cpptraj script, and the files I used
> to prepare the prmtop files in tleap in case that helps.
>
> Best,
> Hunter
>
> --
> Hunter Wilson
> Chemistry PhD Candidate
> Bhagi-Damodaran Group
> wils1872.umn.edu
>
> Department of Chemistry
> University of Minnesota- Twin Cities
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Received on Tue Nov 08 2022 - 11:00:03 PST
